In the vaults of this most famous Polish necropolis are burial crypts with the ashes of Polish kings and their families, deposited here since the time of Sigismund the Old, except the last three monarchs.  The Crypt of Saint Leonard crypt is the resting place of Tadeusz Kościuszko, General Władysław Sikorski, the crypt under the Tower of Silver Bells – Marshal Józef Piłsudski and President Lech Kaczyński with his wife. In the Crypt of the National Bards are the sarcophagi of Adam Mickiewicz and Juliusz Słowacki and an urn containing the ashes of Cyprian Kamil Norwid. Finding his final resting place on Wawel Hill was not easy, especially when Cardinal Adam Sapieha was in charge of the cathedral. He did not like the disruption to the royal character of the place. He did not give his consent for the writer Henryk Sienkiewicz to be buried in the crypts or for the transfer of the remains of the late Marshal Józef Piłsudski from the Crypt of St John the Baptist to the Crypt of St Stanislaus. The construction of the St Leonard's Church under the Tower of the Silver Bells sparked a stormy Wawel conflict.   

The tour of the royal tombs begins in the Crypt of StLeonard. It was built between 1090 and 1117. It is one of the best-preserved Romanesque interiors in Poland. In the middle is the tomb of Bishop Maurus, who died in 1118, found during archaeological work in 1938. In this crypt rest: King Jan III Sobieski, d. 17 June 1696, Queen Maria Kazimiera, d. 1716, King Michał Korybut Wiśniowiecki, d. 10 November 1673, Prince Józef Poniatowski, Tadeusz Kościuszko, d. in Solura, Switzerland, 15 October 1817. In February 1818, permission was obtained from Tsar Alexander I for Kościuszko to be buried at Wawel. It took place on 22-23 June 1818, Gen. Władysław Sikorski, died in a plane crash in Gibraltar on 4 July 1943.

In the Crypt of St Leonard,Fr Karol Wojtyla celebrated his Primate Mass on 2 November 1946 in front of the altar designed by the French architect Viollet-le-Duc. On 9 June 1997, as Pope John Paul II, he celebrated Mass once again on the 50th anniversary of his ordination to the priesthood.

Another one is the cCypt of King Stefan Batory.The king died in Grodno on 12 December 1586. Shortly afterwards, a tin sarcophagus was commissioned for him in the workshop of Daniel Gieseler I, a convict from Gdańsk.

In another rests the family of King Ladislaus IV Vasa. The sarcophagi of the King and his wife Queen Cecilia Renata made of gilded copper are an interesting example of Toruń goldsmithing. Next to the parents rest the children: royal Sigismund Casimir Vasa (died 1647) and royal Anna Maria Izabela (died 1642).

In the crypt, which King Sigismund the Old designated for his family, rest: King Sigismund II August, died in Knyszyn on 7 July 1572, Queen Anne Jagiellon, died in Warsaw on 9 September 1596, Queen Anne of Austria, first wife of Sigismund III Vasa, died on 10 February 1598 in Warsaw, buried in Wawel Cathedral on 16 October 1599, Prince Alexander Charles Vasa, died on 19 November 1634, son of Sigismund III Vasa. Another glass urn contains the ashes of King Stanisław Leszczyński, died 23 February 1766. The urn containing the king's ashes was not placed in the royal tombs until 1938.

Behind the Romanesque wall, three more sarcophagi can be seen: that of Queen Barbara Zápolya, a native of Transylvania, first wife of Sigismund I the Old, died on 2 October 1515; that of Queen Anna Maria Vasa, daughter of Sigismund III Vasa, died on 9 February 1600 in Warsaw; and that of King Augustus II the Strong, died on 1 February 1733.

In the neighbouring crypt, located under the Sigismund Chapel, King Sigismund I the Old, who died on 1 April 1548, is buried in a stone sarcophagus together with his son Olbracht, who died in infancy. The royal sarcophagus was decorated with a medallion bearing the king's image. Bartolommeo Berrecci designed it.

Buried in the Vasa Crypt are King Sigismund III Vasa, died 30 April 1632, and Queen Constance of Austria, second wife of King Sigismund III, died 10 July 1631. The funeral of the royal couple took place at Wawel on 4 July 1633, Cardinal John Albert Vasa, died in Padua on 29 December 1634, buried at Wawel on 26 April 1635, Queen Louise Marie Gonzaga, wife of King John Casimir, died in Warsaw on 10 May 1667, King John Casimir Vasa, died in Nevers, France, on 16 December 1672. His body was brought to Kraków by Bishop Andrzej Trzebicki. The king was buried in the cathedral on 31 January 1676, Prince John Sigismund Vasa son of John Casimir and Louise Maria Gonzaga. Leaving the Vasa Crypt, one passes an urn with soil from Katyń placed in the wall and a commemorative plaque erected in 1990 to mark the 50th anniversary of the Katyń massacre.

In the last crypt, designed by Adolf Szyszko-Bohusz, in the Romanesque tower, rests Marshal Józef Piłsudski, transferred here from the crypt of CCSt Leonard, where he was originally buried.In accordance with his wishes, the Marshal is accompanied by a clay urn with soil from the grave of his mother Maria Piłsudska, née Bilewicz, who is buried, like the Marshal's heart, on the Rossa river in Vilnius. On the walls are commemorative plaques of soldiers, and in the corner – a bust of the chief made by Konstanty Laszczka. The crypt is closed by an openwork grille with the coats of arms of Poland and Lithuania and the Piłsudski family coat of arms.

In the vestibule of this crypt, in the sarcophagus to the left, President Lech Kaczyński and his wife Maria are buried, who died in the Smoleńsk air crash on 10 April 2010; on 10 September 2010, a plaque of pale sandstone with the names of all the victims of the crash and a Latin inscription was unveiled in the vestibule of the crypt: Corpora dormiunt, vigilant animae ('bodies sleep, souls watch').